Get toplevel sequences details

This function retrieves a few extra details about a toplevel sequence. These sequences correspond to genomic regions in the genome assembly that are not a component of another sequence region. Thus, toplevel sequences will be chromosomes and any unlocalised or unplaced scaffolds.

get_toplevel_sequence_info(
  species_name = "homo_sapiens",
  toplevel_sequence = c(1:22, "X", "Y", "MT"),
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

species_name	The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Examples: 'homo_sapiens' (human), 'ovis_aries' (Domestic sheep) or 'capra_hircus' (Goat).
toplevel_sequence	A toplevel sequence name, e.g. chromosome names such as "1", "X", or "Y", or a non-chromosome sequence, e.g., a scaffold such as "KI270757.1".
verbose	Whether to be chatty.
warnings	Whether to print warnings.
progress_bar	Whether to show a progress bar.

Value

A tibble, each row being a toplevel sequence, of 8 variables:

species_name

Ensembl species name: this is the name used internally by Ensembl to uniquely identify a species by name. It is the scientific name but formatted without capitalisation and spacing converted with an underscore, e.g., 'homo_sapiens'.

toplevel_sequence

Name of the toplevel sequence.

is_chromosome

A logical indicating whether the toplevel sequence is a chromosome (TRUE) or not (FALSE).

coord_system

Coordinate system type.

assembly_exception_type

Coordinate system type.

is_circular

A logical indicating whether the toplevel sequence is a circular sequence (TRUE) or not (FALSE).

assembly_name

Assembly name.

length

Genomic length toplevel sequence in base pairs.

See also

get_toplevel_sequences()

Examples

# Get details about human chromosomes (default)
get_toplevel_sequence_info()
#> # A tibble: 25 × 8
#>    species_name toplevel_sequen… is_chromosome coordinate_syst… assembly_except…
#>    <chr>        <chr>            <lgl>         <chr>            <chr>           
#>  1 homo_sapiens 1                TRUE          chromosome       REF             
#>  2 homo_sapiens 2                TRUE          chromosome       REF             
#>  3 homo_sapiens 3                TRUE          chromosome       REF             
#>  4 homo_sapiens 4                TRUE          chromosome       REF             
#>  5 homo_sapiens 5                TRUE          chromosome       REF             
#>  6 homo_sapiens 6                TRUE          chromosome       REF             
#>  7 homo_sapiens 7                TRUE          chromosome       REF             
#>  8 homo_sapiens 8                TRUE          chromosome       REF             
#>  9 homo_sapiens 9                TRUE          chromosome       REF             
#> 10 homo_sapiens 10               TRUE          chromosome       REF             
#> # … with 15 more rows, and 3 more variables: is_circular <lgl>,
#> #   assembly_name <chr>, length <int>

# Get details about a scaffold
# (To find available toplevel sequences to query use the function
# `get_toplevel_sequences()`)
get_toplevel_sequence_info(species_name = 'homo_sapiens', toplevel_sequence = 'KI270757.1')
#> # A tibble: 1 × 8
#>   species_name toplevel_sequence is_chromosome coordinate_syst… assembly_except…
#>   <chr>        <chr>             <lgl>         <chr>            <chr>           
#> 1 homo_sapiens KI270757.1        FALSE         scaffold         REF             
#> # … with 3 more variables: is_circular <lgl>, assembly_name <chr>, length <int>